"Unraveling the Gut Microbiome of the Genus Herichthys (Pisces: Cichlidae): What Can We Learn from Museum Specimens?"

The use of museum preserved specimens to know microbiome in extinct and threatened species has been explored recently. The fishes of the genus Herichthys are distributed mainly in the Pánuco-Tamesí system in Northeastern Mexico, one of the most polluted basins in the country leading to near half of the species be considering as threatened. In this paper we used the hypervariable V4 region of the 16S rRNA gene from the 11 species of the genus Herichthys obtained from museum collections to evaluate the potential use of fixed preserved vouchers in the knowledge of gut microbiota diversity and the potential role of sympatric and allopatric speciation of the hosts in the gut microbiome evolution. The 100% of the samples were successfully amplified where the number of amplicons ranged from 4500 from a formaldehyde fixed specimen up to 55,000 in ethanol preserved specimens. Differences in gut microbiota were found between sympatric species and among the comparison of some trophic guilds. A non-random association between the gut host and their microbiome was found allow to suggest a potential phylosymbiosis relationship. In conclusion, the most abundant phyla recovered from the gut microbiota in this study were similar to those previously reported in other cichlids supporting the idea that a gut microbial core is conserved in this group of fishes despite millions of years of evolution and leading to support the potential use of museum specimens in microbiome studies.

Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene.

This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.

Tapirus bairdii-Associated Fecal Microbiome from a Critical Conservation Area: Calakmul, México.

Baird's tapir (Tapirus bairdii) is the largest native terrestrial mammal in the Neotropics, which is endangered primarily as a consequence of habitat loss and overhunting. Baird's tapir is predominantly nocturnal and exists at low densities which complicates field studies. Baird's tapir is a large-bodied herbivore that plays a key role in maintaining healthy tropical forests through seed dispersal in its feces. Studies of gut microbiome are essential and valuable to assess the health status of the host and the interaction with the environment. In this study, we collected fresh fecal samples of T. bairdii to analyze its gut microbiome during the rainy and dry seasons in the Calakmul region, which is a critical rainforest conservation area in Mexico. The results of a high-throughput 16S rDNA gene sequencing approach suggest that the fecal microbiome of Baird's tapir has no significant differences in composition among seasons. The most common phyla were Firmicutes, Bacteroidetes, Proteobacteria, Kiritimatiellaeota, and Spirochaetes. This study suggests that the stability of the fecal microbiome is related to similar feeding strategies throughout the year, and emphasizes the value of tapir in seed dispersal (and associated microbes) to the well-conserved forests of the Greater Calakmul region as biodiversity hotspots for conservation.

Alveolar microbiota profile in patients with human pulmonary tuberculosis and interstitial pneumonia.

BACKGROUND: The presence of the human lung microbiota has been demonstrated in patients with different lung diseases, mainly in sputum samples. However, for study of the alveolar microbiota, a bronchoalveolar lavage (BAL) sample represents the lower respiratory tract (LRT) environment. It is currently unknown whether there is a specific alveolar microbiota profile in human lung diseases, such as pulmonary tuberculosis (TB) and interstitial pneumonia (IP). METHODS: BAL samples from six active TB patients, six IP patients and ten healthy volunteers were used for DNA extraction followed by amplification of the complete bacterial 16S ribosomal RNA gene (16S rDNA). The 16S rDNA was sequenced with a MiSeq Desktop Sequencer, and the data were analysed by QIIME software for taxonomic assignment. RESULTS: The alveolar microbiota in TB and IP patients and healthy volunteers was characterized by six dominant phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria and Cyanobacteria. A significant reduction in the abundance of Firmicutes was observed in IP patients. In TB and IP patients, the diversity of the alveolar microbiota was diminished, characterized by a significant reduction in the abundance of the Streptococcus genus and associated with increased Mycobacterium abundance in TB patients and diminished Acinetobacter abundance in IP patients with respect to their abundances in healthy volunteers. However, an important difference was observed between TB and IP patients: the Fusobacterium abundance was significantly reduced in TB patients. Exclusive genera that were less abundant in patients than in healthy volunteers were characterized for each study group. CONCLUSIONS: This study shows that the alveolar microbiota profile in BAL samples from TB and IP patients, representing infectious and non-infectious lung diseases, respectively, is characterized by decreased diversity.

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake.

Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.

Habitat conditions drive phylogenetic structure of dominant bacterial phyla of microbialite communities from different locations in Mexico.

Community structure and composition are dictated by evolutionary and ecological assembly processes which are manifested in signals of, species diversity, species abundance and species relatedness. Analysis of species coexisting relatedness, has received attention as a tool to identify the processes that influence the composition of a community within a particular habitat. In this study, we tested if microbialite genetic composition is dependent on random events versus biological/abiotical factors. This study was based on a large genetic data set of two hypervariable regions (V5 and V6) from previously generated barcoded 16S rRNA amplicons from nine microbialite communities distributed in Northeastern, Central and Southeastern Mexico collected in May and June of 2009. Genetic data of the most abundant phyla (Proteobacteria, Planctomycetes, Verrucomicrobia, Bacteroidetes, and Cyanobacteria) were investigated in order to state the phylogenetic structure of the complete communities as well as each phylum. For the complete dataset, Webb NTI index showed positive and significant values in the nine communities analysed, where values ranged from 31.5 in Pozas Azules I to 57.2 in Bacalar Pirate Channel; meanwhile, NRI index were positive and significant in six of the nine communities analysed with values ranging from 18.1 in Pozas Azules I to 45.1 in Río Mesquites. On the other hand, when comparing each individual phylum, NTI index were positive and significant in all groups, except in Cyanobacteria for which positive and significant values were only found in three localities; finally, NRI index was significant in only a few of the comparisons performed. The results suggest that habitat filtering is the main process that drives phylogenetic structure in bacterial communities associated to microbialites with the exception of Cyanobacteria where different lineages can contribute to microbialite formation and growth.

Prevalence and transmission of the most relevant zoonotic and vector-borne pathogens in the Yucatan peninsula: A review.

BACKGROUND: Habitat modification and land use changes impact ecological interactions and alter the relationships between humans and nature. Mexico has experienced significant landscape modifications at the local and regional scales, with negative effects on forest cover and biological biodiversity, especially in the Yucatan peninsula in southeastern Mexico. Given the close relationship between landscape modification and the transmission of zoonotic and vector-borne diseases, it is essential to develop criteria for identifying priority zoonoses in the south of the country. METHODOLOGY/PRINCIPAL FINDINGS: We reviewed 165 published studies on zoonotic and vector-borne diseases in the region (2015-2024). We identified the most frequent vectors, reservoirs, and hosts, the most prevalent infections, and the factors associated with transmission risk and the anthropogenic landscape modification in urban, rural, ecotone, and sylvatic habitats. The most relevant pathogens of zoonotic risk included Trypanosoma cruzi, arboviruses, Leishmania, Rickettsia, Leptospira, and Toxoplasma gondii. Trypanosoma cruzi was the vector-borne agent with the largest number of infected vertebrate species across habitats, while Leishmania and arboviruses were the ones that affected the greatest number of people. Dogs, cats, backyard animals, and their hematophagous ectoparasites are the most likely species maintaining the transmission cycles in human settlements, while rodents, opossums, bats, and other synanthropic animals facilitate connection and transmission cycles between forested habitats with human-modified landscapes. Pathogens displayed different prevalences between the landscapes, T. cruzi, arbovirus, and Leptospira infections were the most prevalent in urban and rural settlements, whereas Leishmania and Rickettsia had similar prevalence across habitats, likely due to the diversity and abundance of the infected vectors involved. The prevalence of T. gondii and Leptospira spp. may reflect poor hygiene conditions. Additionally, results suggest that prevalence of zoonotic and vector-borne diseases is higher in deforested areas and agricultural aggregates, and in sites with precarious health and infrastructure services. CONCLUSIONS: Some hosts, vectors, and transmission trends of zoonotic and vector-borne diseases in the YP are well known but others remain poorly recognized. It is imperative to reinforce practices aimed at increasing the knowledge, monitoring, prevention, and control of these diseases at the regional level. We also emphasize the need to perform studies on a larger spatio-temporal scale under the socio-ecosystem perspective, to better elucidate the interactions between pathogens, hosts, vectors, environment, and sociocultural and economic aspects in this and many other tropical regions.

Environmental and Mineralogical Controls on Biosignature Preservation in Magnesium Carbonate Systems Analogous to Jezero Crater, Mars.

Jezero Crater on Mars is a paleolacustrine environment where Mg-carbonates may host evidence of ancient life. To elucidate the environmental and mineralogical controls on biosignature preservation, we examined samples from five terrestrial analogs: Lake Salda (Turkey), Lake Alchichica (Mexico), Qinghai-Tibetan Plateau (China), Mg-carbonate playas (British Columbia, Canada), and a mine with fine-grained ultramafic tailings (Yukon, Canada). The mineralogical compositions of the samples varied, yet were often dominated by either aragonite (CaCO3) or hydromagnesite [Mg5(CO3)4(OH)2·4H2O]. Aragonite-rich samples from Alchichica, Mg-carbonate playas, and the ultramafic mine contained an abundance of entombed microbial biomass, including organic structures that resembled cells, whereas hydromagnesite-rich samples were devoid of microfossils. Aragonite often precipitates subaqueously where microbes thrive, thereby increasing the likelihood of biomass entombment, while hydrated Mg-carbonates typically form by evaporation in subaerial settings where biofilms are less prolific. Magnesite (MgCO3), the most stable Mg-carbonate, forms extremely slowly, which may limit the capture of biosignatures. Hydrated Mg-carbonates are prone to transformation via coupled dissolution-precipitation reactions that may expose biosignatures to degradation. Although less abundant, aragonite is commonly found in Mg-carbonate environments and is a better medium for biosignature preservation due to its fast precipitation rates and relative stability, as well as its tendency to form subaqueously and lithify. Consequently, we propose that aragonite be considered a valuable exploration target on Mars.

Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico.

Mangroves are unique coastal ecosystems, which have many important ecological functions, as they are a reservoir of many marine species well adapted to saline conditions and are fundamental as sites of carbon storage. Although the microbial contribution to nutrient cycling in these ecosystems has been well recognized, there is a lack of information regarding the microbial composition and structure of different ecological types of mangrove forests. In this study, we characterized the microbial community (Bacteria and Archaea) in sediments associated with five ecological types of mangrove forests in a coastal lagoon dominated by Avicennia germinans and Rhizophora mangle, through 16S rRNA-V4 gene sequencing. Overall, Proteobacteria (51%), Chloroflexi (12%), Gemmatimonadetes (5%) and Planctomycetes (6%) were the most abundant bacterial phyla, while Thaumarchaeota (30%), Bathyarchaeota (21%) and Nanoarchaeaeota (18%) were the dominant archaeal phyla. The microbial composition associated with basin mangroves dominated by Avicennia germinans was significantly different from the other ecological types, which becomes relevant for restoration strategies.

Similar connectivity of gut microbiota and brain activity networks is mediated by animal protein and lipid intake in children from a Mexican indigenous population.

The gut microbiota-brain axis is a complex communication network essential for host health. Any long-term disruption can affect higher cognitive functions, or it may even result in several chronic neurological diseases. The type and diversity of nutrients an individual consumes are essential for developing the gut microbiota (GM) and the brain. Hence, dietary patterns might influence networks communication of this axis, especially at the age that both systems go through maturation processes. By implementing Mutual Information and Minimum Spanning Tree (MST); we proposed a novel combination of Machine Learning and Network Theory techniques to study the effect of animal protein and lipid intake on the connectivity of GM and brain cortex activity (BCA) networks in children from 5-to 10 years old from an indigenous community in the southwest of México. Socio-ecological conditions in this nonwestern lifestyle community are very homogeneous among its inhabitants but it shows high individual heterogeneity in the consumption of animal products. Results suggest that MST, the critical backbone of information flow, diminishes under low protein and lipid intake. So, under these nonwestern regimens, deficient animal protein and lipid consumption diets may significantly affect the GM-BCA connectivity in crucial development stages. Finally, MST offers us a metric that unifies biological systems of different nature to evaluate the change in their complexity in the face of environmental pressures or disturbances. Effect of Diet on gut microbiota and brain networks connectivity.

Changes in the sediment microbial community structure of coastal and inland sinkholes of a karst ecosystem from the Yucatan peninsula.

The karst underground river ecosystem of Yucatan peninsula is composed of cave systems and sinkholes. The microbial diversity of water from this underground river has been studied, but, structure of the microbial community in its cave sediments remained largely unknown. Here we describe how the microbial community structure of these sediments changes due to different environmental conditions found in sediment zones along the caves of a coastal and an inland sinkhole. We found that dominant microbial groups varied according to the type of sinkhole (Coastal: Chloroflexi and Crenarchaeota; inland: Methylomirabilota and Acidobacteriota) and that the community structures differed both among sinkhole types, and within the sediment zones that were studied. These microorganisms are associated with different types of metabolism, and differed from a microbial community dominated by sulfate reducers at the coastal sinkhole, to one dominated by methylotrophs at the inland sinkhole, suggesting there are biogeochemical processes in the coastal and inland sinkholes that lead to changes in the microbial composition of the underground river ecosystem's sediments. Our results suggest sediments from unexplored sinkhole caves are unique environmental niches with distinct microbial assemblages that putatively play an important role in the biogeochemical cycles of these ecosystems.

Shifts in water column microbial composition associated to lakes with different trophic conditions: "Lagunas de Montebello" National Park, Chiapas, México.

Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the "Lagunas de Montebello" National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine.

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment.

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D ß-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.

The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

The microbiome of modern microbialites in Bacalar Lagoon, Mexico.

Microbialites are highly diverse microbial communities that represent modern examples of the oldest life forms, stromatolites (dated >3.7 Ga). Bacalar Lagoon, in Mexico, harbors the largest freshwater microbialite occurrences of the world; yet diverse anthropogenic activities are changing the oligotrophic conditions of the lagoon. The objective of this work was to perform a spatial exploration of the microbialites of Bacalar Lagoon, analyze their prokaryote diversity, following a high throughput sequencing approach of the V4 region of the 16S rDNA, and correlate to the environmental parameters that influence the structure of these communities. The results indicate the presence of microbialites throughout the periphery of the lagoon. The microbiome of the microbialites is composed primarily of Proteobacteria (40-80%), Cyanobacteria (1-11%), Bacteroidetes (7-8%), Chloroflexi (8-14%), Firmicutes (1-23%), Planctomycetes (1-8%), and Verrucomicrobia (1-4%). Phylogenetic distance analyses suggests two distinct groups of microbialites associated with regions in the lagoon that have differences in their environmental parameters, including soluble reactive silicate (in the north), bicarbonates and available forms of nitrogen (ammonium, nitrates and nitrites) (in the south). These microbialite groups had differences in their microbiome composition associated to strong anthropogenic pressure on water quality (agriculture, landfill leachate, lack of water treatment infrastructure and intensive tourism), which were related to a loss of microbial diversity.

Geographical separation and physiology drive differentiation of microbial communities of two discrete populations of the bat Leptonycteris yerbabuenae.

In this paper, we explore how two discrete and geographically separated populations of the lesser long-nosed bat (Leptonycteris yerbabuenae)-one in central and the other in the Pacific region of Mexico-differ in their fecal microbiota composition. Considering the microbiota-host as a unity, in which extrinsic (as food availability and geography) or intrinsic factors (as physiology) play an important role in the microbiota composition, we would expect differentiation in the microbiota of two geographically separated populations. The Amplicon Sequences Variants (ASVs) of the V4 region of the 16s rRNA gene from 68 individuals were analyzed using alpha and beta diversity metrics. We obtained a total of 11 566 (ASVs). The bacterial communities in the Central and Pacific populations had a diversity of 6,939 and 4,088 ASVs, respectively, sharing a core microbiota of 539 ASVs accounting for 75% of the relative abundance, suggesting stability over evolutionary time. The Weighted UniFrac metrics tested by a PERMANOVA showed that lactating and pregnant females had significant beta diversity differences in the two populations compared with other reproductive stages. This could be a consequence of the increased energy requirements of these physiological stages, more than the variation due to geographical separation. In contrast, a positive correlation of the observed ASVs of fecal microbiota with the observed ASVs of plastids related to the diet was observed in the juveniles and adults, suggesting that in these physiological stages an extrinsic factor as the diet shapes the microbiota composition. The results provide a baseline for future studies of the microbiome in these two wild populations of the lesser long-nosed bat, the main pollinator of the Agaves from which the beverages tequila and mezcal are made.

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes.

The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., "Westernized" (México City, n = 13) and "non-Westernized" (Me'phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me'phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me'phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.

Temporal analysis of the microbial communities in a nitrate-contaminated aquifer and the co-occurrence of anammox, n-damo and nitrous-oxide reducing bacteria.

Groundwater-N pollution derives from agricultural and urban activities, and compromises water quality in shallow aquifers, putting human and environmental health at risk. Nonetheless, subsurface microbiota can transform dissolved inorganic nitrogen into N2. In this study, we surveyed the microbial community of a shallow aquifer by sampling one well, one piezometer and a spring within an agricultural area that receives N-inputs of more than 700 kg/ha per year through irrigation with wastewater. The survey was conducted during a year with a 16S rRNA next-gen approach. In parallel, we quantified the number of gene copies and transcripts related to anaerobic ammonium oxidation (anammox, hzo), nitrite-dependent anaerobic methane oxidation (n-damo, nod and pmoA) and nitrous oxide reduction (last step of denitrification, nosZ), during the dry and rainy seasons. Our results showed that the groundwater samples had 17.7 to 22.5 mg/L of NO3--N. The bacterial and archaeal community structure was distinctive at each site, and it remained relatively stable over time. We verified the co-occurrence of N-transforming bacteria, which was correlated with the concentration of NO2-/NO3- and ORP/DO values (DO: ~3.0 mg/L). Our analyses suggest that these conditions may allow the presence of nitrifying microorganisms which can couple with anammox, n-damo and denitrifying bacteria in interrelated biogeochemical pathways. Gene density (as the number of gene copies per litre) was lower in the rainy season than in the dry season, possibly due to dilution by rainwater infiltration. Yet, the numbers of hzo gene copies here found were similar to those reported in oceanic oxygen minimum zones and in a carbonate-rock aquifer. The transcript sequences showed that Candidatus Brocadia spp. (anammox), Candidatus Methylomirabilis spp. (n-damo) and autotrophic denitrifying Betaproteobacteria coexist in the groundwater environment, with the potential to attenuate the concentration of dissolved inorganic nitrogen by reducing it to N2 rather than N2O; delivering thus, an important ecosystem service to remove contaminants.

Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression.

If you think you are in control of your behavior, think again. Evidence suggests that behavioral modifications, as development and persistence of depression, maybe the consequence of a complex network of communication between macro and micro-organisms capable of modifying the physiological axis of the host. Some parasites cause significant nutritional deficiencies for the host and impair the effectiveness of cognitive processes such as memory, teaching or non-verbal intelligence. Bacterial communities mediate the establishment of parasites and vice versa but this complexity approach remains little explored. We study the gut microbiota-parasite interactions using novel techniques of network analysis using data of individuals from two indigenous communities in Guerrero, Mexico. Our results suggest that Ascaris lumbricoides induce a gut microbiota perturbation affecting its network properties and also subnetworks of key species related to depression, translating in a loss of emergence. Studying these network properties changes is particularly important because recent research has shown that human health is characterized by a dynamic trade-off between emergence and self-organization, called criticality. Emergence allows the systems to generate novel information meanwhile self-organization is related to the system's order and structure. In this way, the loss of emergence means a depart from criticality and ultimately loss of health.

Metabolic symbiosis and the birth of the plant kingdom.

Eukaryotic cells are composed of a variety of membrane-bound organelles that are thought to derive from symbiotic associations involving bacteria, archaea, or other eukaryotes. In addition to acquiring the plastid, all Archaeplastida and some of their endosymbiotic derivatives can be distinguished from other organisms by the fact that they accumulate starch, a semicrystalline-storage polysaccharide distantly related to glycogen and never found elsewhere. We now provide the first evidence for the existence of starch in a particular species of single-cell diazotrophic cyanobacterium. We provide evidence for the existence in the eukaryotic host cell at the time of primary endosymbiosis of an uridine diphosphoglucose (UDP-glucose)-based pathway similar to that characterized in amoebas. Because of the monophyletic origin of plants, we can define the genetic makeup of the Archaeplastida ancestor with respect to storage polysaccharide metabolism. The most likely enzyme-partitioning scenario between the plastid's ancestor and its eukaryotic host immediately suggests the precise nature of the ancient metabolic symbiotic relationship. The latter consisted in the export of adenosine diphosphoglucose (ADP-glucose) from the cyanobiont in exchange for the import of reduced nitrogen from the host. We further speculate that the monophyletic origin of plastids may lie in an organism with close relatedness to present-day group V cyanobacteria.